Hey there, monks. I think i'm having a buffering issue since i need to read and parse big text files (created by myself in previous lines of the code) to finally print things in another file. At some point, after reading a file with 90855 lines, the script is not reading a line of the next file completely. I have counted the number of characters read until this happens: 233467, and therefore tried to flush the buffer and sleep before reading the next line of the file. Doesn't work. Any suggestion, please? thanks a lot. The part of the code coming: 

for my $o (0..1){
  if ($o==0){
    @files = reverse <*_SITES_3utr>;
  }else{
    @files = reverse <*_SITES_cds>;
  }
undef(%pita_sites_nu);undef(%pita_tot_score);my($comp_p);undef(%allowe
+d_wobbles);#undef(%site_nu);
foreach $i(@files){
   my $buff=0;
  print "Analyzing $i\n";sleep(1);
  $program= $1 if $i=~ /(\w+)_SITES/;
  open(FIL, $i) or die "$!: $i\n";
  while(<FIL>){

    $buff += length($_); if ($buff >= 230000){$buff=0;sleep(1);select(
+(select(FIL), $|=1)[0]);} #FLUSH THE BUFFER, NOT WORKING!!!
                           
    undef($a);
    unless($.== 1){
      if ($o==0){
        if (/^\d+\t(\S+)\t(\S+)\t(\d+)\t(\d+)\t(\S+)\t(\S+)\t(.*)/){
          $mirna= $1; $target= $2; $start= $3; $end= $4; $site= $5; $c
+omp_p= $6;$a= $7;$j= "${mirna}_${target}_${start}_$end";
          $site_nu{$j}= "$mirna\t$target\t$start\t$end\t$site\t$comp_p
+";#Store each site in a hash
        }else{die "$buff characters, in line $.:$_\n"} #DIES HERE!!!
      }else{
        if (/^\d+\t(\S+)\t(\S+)\t(\d+)\t(\d+)\t(\S+)\t(.*)/){
          $mirna= $1; $target= $2; $start= $3; $end= $4; $site= $5;$a=
+ $6;$j= "${mirna}_${target}_${start}_$end";
          $site_nu{$j}= "$mirna\t$target\t$start\t$end\t$site";#Store 
+each site in a hash
        }
      }

[download]

It dies at the "DIES HERE!!" die, after reading 3413 characters of the second file. Happens because the regex doesn't work since only half of the line is in $_. Help please! Thanks again.

In reply to buffering issue? by dannyjmh

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